I don't know the very details, but what you are experiencing seems logical to me:
Stage video uses native video rendering from the GPU. Essentially, it punches a whole in your Flash app and renders the video there. It is not managed by Flash, but by the OS.
You may want to look into that fact, and how StageVideo actually operates.
Actually, I looked briefly at the dev guide this week end, and Stage Video actually renders from the GPU under the Actionscript App.
It could be something like this:
Stage video is behind the Actionscript objects and one of them is as big or bigger than the video rendering rectangle and it is grabbing mouse interaction.
Also, I'm not certain StageVideo can recieve mouse events...
Hope this helps.